Slc10a4 (solute carrier family 10, member 4) - Rat Genome Database

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Gene: Slc10a4 (solute carrier family 10, member 4) Rattus norvegicus
Analyze
Symbol: Slc10a4
Name: solute carrier family 10, member 4
RGD ID: 1309536
Description: Predicted to enable bile acid:sodium symporter activity. Predicted to be involved in bile acid and bile salt transport and regulation of neurotransmitter loading into synaptic vesicle. Predicted to act upstream of or within adult behavior and response to xenobiotic stimulus. Predicted to be located in plasma membrane. Predicted to be active in several cellular components, including dopaminergic synapse; serotonergic synapse; and synaptic vesicle membrane. Orthologous to human SLC10A4 (solute carrier family 10 member 4); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; copper atom.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: bile acid transporter Slc10a4; LOC305309; Na(+)/bile acid cotransporter 4; sodium/bile acid cotransporter 4; solute carrier family 10 (sodium/bile acid cotransporter family), member 4; solute carrier family 10 member 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21435,198,509 - 35,203,729 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1435,197,886 - 35,203,729 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1435,562,389 - 35,567,613 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01436,867,146 - 36,872,370 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01435,355,472 - 35,360,696 (-)NCBIRnor_WKY
Rnor_6.01437,764,839 - 37,770,059 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1437,764,839 - 37,770,059 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01437,575,344 - 37,580,564 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41437,603,484 - 37,608,704 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11437,605,918 - 37,611,139 (-)NCBI
Celera1434,453,572 - 34,458,796 (-)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:18355966   PMID:21742018   PMID:23022458   PMID:25176177  


Genomics

Comparative Map Data
Slc10a4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21435,198,509 - 35,203,729 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1435,197,886 - 35,203,729 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1435,562,389 - 35,567,613 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01436,867,146 - 36,872,370 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01435,355,472 - 35,360,696 (-)NCBIRnor_WKY
Rnor_6.01437,764,839 - 37,770,059 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1437,764,839 - 37,770,059 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01437,575,344 - 37,580,564 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41437,603,484 - 37,608,704 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11437,605,918 - 37,611,139 (-)NCBI
Celera1434,453,572 - 34,458,796 (-)NCBICelera
Cytogenetic Map14p11NCBI
SLC10A4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38448,483,343 - 48,489,526 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl448,483,343 - 48,489,526 (+)EnsemblGRCh38hg38GRCh38
GRCh37448,485,360 - 48,491,543 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36448,180,206 - 48,185,921 (+)NCBINCBI36Build 36hg18NCBI36
Build 34448,326,376 - 48,332,092NCBI
Celera448,934,151 - 48,940,332 (+)NCBICelera
Cytogenetic Map4p11NCBI
HuRef447,805,548 - 47,811,582 (+)NCBIHuRef
CHM1_1448,484,515 - 48,490,696 (+)NCBICHM1_1
T2T-CHM13v2.0448,450,381 - 48,456,560 (+)NCBIT2T-CHM13v2.0
Slc10a4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39573,164,247 - 73,170,298 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl573,164,226 - 73,170,298 (+)EnsemblGRCm39 Ensembl
GRCm38573,006,904 - 73,012,955 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl573,006,883 - 73,012,955 (+)EnsemblGRCm38mm10GRCm38
MGSCv37573,398,143 - 73,404,194 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36573,286,039 - 73,292,090 (+)NCBIMGSCv36mm8
Celera570,259,481 - 70,265,532 (+)NCBICelera
Cytogenetic Map5C3.2NCBI
Slc10a4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544719,189,262 - 19,194,412 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544719,189,516 - 19,194,982 (-)NCBIChiLan1.0ChiLan1.0
SLC10A4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1484,391,103 - 84,402,422 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl484,391,103 - 84,402,422 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0473,663,681 - 73,669,852 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SLC10A4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11344,293,956 - 44,299,529 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1344,277,094 - 44,299,732 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1344,247,450 - 44,253,276 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01344,898,294 - 44,903,727 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1344,898,966 - 44,903,921 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11344,572,619 - 44,578,253 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01344,105,676 - 44,113,317 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01344,987,655 - 44,993,299 (+)NCBIUU_Cfam_GSD_1.0
Slc10a4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528531,795,835 - 31,801,849 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648214,496,386 - 14,502,957 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493648214,496,386 - 14,502,313 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC10A4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl838,378,872 - 38,385,863 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1838,378,878 - 38,385,748 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2840,414,352 - 40,419,674 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC10A4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1271,763,028 - 1,769,246 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl271,762,568 - 1,769,056 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604747,765,658 - 47,771,896 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc10a4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476118,489,683 - 18,495,507 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476118,489,636 - 18,495,607 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc10a4
10 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:72
Count of miRNA genes:66
Interacting mature miRNAs:68
Transcripts:ENSRNOT00000029721
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143076702539153750Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 41 1
Low 3 4 10 2 2 33 18
Below cutoff 29 18 11 17 11 2 3 5 17 9 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000029721   ⟹   ENSRNOP00000037495
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1435,197,886 - 35,203,729 (-)Ensembl
Rnor_6.0 Ensembl1437,764,839 - 37,770,059 (-)Ensembl
RefSeq Acc Id: NM_001008555   ⟹   NP_001008555
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21435,198,509 - 35,203,729 (-)NCBI
Rnor_6.01437,764,839 - 37,770,059 (-)NCBI
Rnor_5.01437,575,344 - 37,580,564 (-)NCBI
RGSC_v3.41437,603,484 - 37,608,704 (-)RGD
Celera1434,453,572 - 34,458,796 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001008555 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAV80706 (Get FASTA)   NCBI Sequence Viewer  
  AAW30131 (Get FASTA)   NCBI Sequence Viewer  
  Q5PT56 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001008555   ⟸   NM_001008555
- UniProtKB: F1LQG5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000037495   ⟸   ENSRNOT00000029721

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5PT56-F1-model_v2 AlphaFold Q5PT56 1-437 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309536 AgrOrtholog
BioCyc Gene G2FUF-15860 BioCyc
Ensembl Genes ENSRNOG00000026091 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000037495 ENTREZGENE
  ENSRNOP00000037495.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029721 ENTREZGENE
  ENSRNOT00000029721.2 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1530.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro BilAc:Na_symport/Acr3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Bilac:Na_transpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na+/solute_symporter_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SLC10A4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:305309 UniProtKB/Swiss-Prot
NCBI Gene 305309 ENTREZGENE
PANTHER PTHR10361 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10361:SF41 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SBF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc10a4 PhenoGen
UniProt F1LQG5 ENTREZGENE, UniProtKB/TrEMBL
  NTCP4_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-02 Slc10a4  solute carrier family 10, member 4  Slc10a4  solute carrier family 10 (sodium/bile acid cotransporter family), member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Slc10a4  solute carrier family 10 (sodium/bile acid cotransporter family), member 4  Slc10a4_predicted  solute carrier family 10 (sodium/bile acid cotransporter family), member 4 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Slc10a4_predicted  solute carrier family 10 (sodium/bile acid cotransporter family), member 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED